WiX installer not working after reboot

I have discovered a problem with our WiX (v3.9) installer just in time for release (of course). We have a custom WPF bootstrapper application that requires .Net 4 to run. The steps to reproduce the problem on a clean Windows 7 x64 installation are as follows:

1. Start the installer. Since .Net 4 is not installed the default bootstrapper for .Net 4 (Full package) starts instead and I choose to install it.

2. When the .Net 4 installation completes I have to reboot the computer.

3. After the computer has rebooted our installer is automatically resumed. After clicking through all the steps of the installation and finally start installing I am told the installation failed. However when I check the "Program and Features" list there is an entry for our application but it is obvious that the application is not installed (no files were installed).

Here is the error stored in the log:

[07DC:07D8][2015-06-03T13:45:55]i300: Apply begin
[0688:07A4][2015-06-03T13:45:55]i360: Creating a system restore point.
[0688:07A4][2015-06-03T13:46:00]i361: Created a system restore point.
[07DC:0BA8][2015-06-03T13:46:00]i336: Acquiring container: WixAttachedContainer, copy from: C:\ProgramData\Package Cache\{f2234eba-50ab-42cd-a6bf-dca86e2f3fce}\MyInstall.exe
[07DC:0BA8][2015-06-03T13:46:00]i000: Setting string variable 'WixBundleLastUsedSource' to value 'C:\ProgramData\Package Cache\{f2234eba-50ab-42cd-a6bf-dca86e2f3fce}\'
[07DC:0BB4][2015-06-03T13:46:00]e000: Error 0x80070001: Failed to extract all files from container, erf: 1:2:0
[07DC:0BA8][2015-06-03T13:46:00]e000: Error 0x80070001: Failed to wait for operation complete.
[07DC:0BA8][2015-06-03T13:46:00]e000: Error 0x80070001: Failed to open container.
[07DC:0BA8][2015-06-03T13:46:00]e000: Error 0x80070001: Failed to open container: WixAttachedContainer.
[07DC:0BA8][2015-06-03T13:46:00]e312: Failed to extract payloads from container: WixAttachedContainer to working path: C:\Users\testuser\AppData\Local\Temp\{f2234eba-50ab-42cd-a6bf-dca86e2f3fce}\7B32FBD553AC13EB47FDA0D0B59B78C0FE57C7F6, error: 0x80070001.
[07DC:07D8][2015-06-03T13:46:00]e000: Error 0x80070001: Failed while caching, aborting execution.
[07DC:07D8][2015-06-03T13:46:00]i000: [ ApplyComplete ] Failed -2147024895
[07DC:07D8][2015-06-03T13:46:00]i399: Apply complete, result: 0x80070001, restart: None, ba requested restart:  No
[07DC:07D8][2015-06-03T13:46:03]i500: Shutting down, exit code: 0x80070001

From what I have found on google people are referring to the bootstrapper not being signed when this error occures, but we have never signed it in the past and we have no certificate so I am thinking it must be something else. What is new with this installer is that we are handling x64 files.

If I exit the installer when it is automatically resumed after the reboot, and then start the installer again everything works. If it makes any difference the installer installs the following packages:

1. Visual C++ 10.0 SP1 Redist (x86)
2. Visual C++ 10.0 SP1 Redist (x64)
3. MyApplication.msi (x64, contains both 32-bit and 64-bit files)

If I run the installer again after the error has occured I can see in the log that the bundle is detected as installed but all of the packages in the chain are absent.

Any ideas what can be the problem and how to fix it? I appreciate any help.